To calibrate this way, first open the `Preview' window and click the `Wedges'
toggle button. The `Wedge calibration' panel will pop up. Mount three
pairs of wedges on the calibration frame: one at the centre of the top
wire, the other two near the bottom corners of the cropped B-scan, as
it appears in the `Preview' window. Put the frame in the water tank,
fill the tank with water at around 50 degrees Celsius, and mount the
probe on the phantom.

The principle of operation is that the ultrasound beam is manually
aligned with the plane of the wires, using the wedges to guage the
local alignment. First, adjust the x and y stages until the top
wedge-pair is near the top centre of the B-scan in the `Preview'
window. Set the ultrasound focus for the top wedge-pair. Set the
time-gain control to highlight the wedges and suppress the rest of the
B-scan. Adjust the z stage until the echos from the two top wedges
appear at the same depth. The ultrasound beam is now roughly aligned
with the top wedge-pair.

Next, adjust the yaw and pitch stages until the bottom wedge-pairs
are aligned with the beam. The echos from the left and right wedge in
each pair should look more or less the same, without any obvious
asymmetry between left and right. The ultrasound beam is now roughly
aligned with all three wedge-pairs: to fine tune the alignment, we're
going to use some image processing tools.

Use the left mouse button to click and drag a bounding box around
each wedge-pair. Click first at the top centre of the wedge-pair, then drag
towards one of the bottom corners. Two indicators of wedge alignment
appear. The first comprises a pair of cyan horizontal lines, each
centred on a wedge's echo. As you adjust the z stage, you should find
that the echos, and hence the cyan lines, move up and down with
respect to each other. The ultrasound beam is centred on the wedges
when the lines are level.

The second alignment indicator comprises a number, displayed in
green near the bottom of the bounding box, quantifying the difference
between the reflections in the left and right halves of the bounding
box. Small numbers indicate small differences and therefore good
alignment. Towards the top of the bounding box is another green
number, which is the smallest difference found so far.

The horizontal cyan lines work well when the ultrasound beam is
narrow compared with the size of the wedges. This is usually the case
for the top wedge-pair, less so for the bottom pairs. When the beam is
so wide that the wedges lie entirely inside it, like at the bottom of
the B-scan in the picture above, you'll find that the cyan lines are
not helpful and you should instead use the green numbers: you're
looking to make them as small as possible.

Start by fine tuning the alignment of the top wedge-pair, by
adjusting the z stage until the cyan lines are level. To calibrate the
probe, the system needs to know the precise location of this pair's
central axis. To find this, move the z stage away from its aligned
position until the bounding box's red centre-line becomes
dashed. Since the wedges now show up as two distinct blobs, the system
can analyse the echos to find their central axis. After a few seconds,
the centre-line turns green. Now adjust the z stage back towards its
aligned position and out the other side, until the centre-line is
dashed again. After a few seconds, the centre-line turns cyan. The
central axis is now fixed. Return the z stage to its aligned position.

Next, set the ultrasound machine's focus for the bottom wedges and
fine tune their alignment. Unless you have a "2.5D" probe with a very
narrow beam, you'll probably want to use the green difference
indicators and not the cyan lines. Adjust only the yaw and pitch
stages until both green numbers are as small as possible (or both sets
of cyan lines are level). Do not touch the z stage, since this will
disturb the alignment of the top wedge-pair. When you're finished, the
`Preview' window should look something like this.

Finally, we need to segment the wires supporting the wedges. Each
pair of wedges is actually supported by two wires: it's the upper of
these two that we're interested in. With the middle mouse button,
click on the upper wire to the left and right of the top
wedge-pair. The system draws a red line through the two points. Next,
again with the middle mouse button, click on one point on the upper of
the two wires supporting the bottom wedges: the system draws a red
line through this point, parallel to the top line. If you click in the
wrong positions, simply click again with the middle mouse
button. Likewise, if you get the wedge bounding boxes wrong, you can
delete a wedge with the right mouse button, then re-define it. The
`Preview' window should now look something like this.

One last detail is to tell the system whether the B-scan is
flipped left/right or not. At the top of the `Preview' window, in red,
are the letters `L' and `R'. Dip your finger into the water tank and
wiggle it about somewhere above the bottom left wedge-pair (left as
your face the phantom). Does your finger appear at the left of the
B-scan in the `Preview' window? If yes, then the B-scan is not flipped
and there's no need to do anything. But if your finger shows up at the
right of the B-scan, then move the mouse into the `Preview' window and
press the space bar. The `L' and `R' will swap around, as in the
picture above, to indicate a flipped left/right B-scan.

Now, read the micrometers and enter the values into the `Wedge
calibration' panel using the five sliders. You also need to tell the
system which wires the wedges are mounted on. To do this, simply count
down the holes from the top of the frame. Remember that each wedge is
supported by two wires, and it's the upper of the two we're interested
in. The top wedge-pair is always mounted on the top two wires: the
lower wedges are mounted to suit the depth range of the probe you're
calibrating. In the example above, the bottom wedges were mounted on
wires strung between the 7th and 8th holes from the top of the frame:
hence, the slider is set to 7.

With all the sliders set, you can now press the `Calculate
calibration' button to work out the spatial calibration. This button
is insensitive until the panel has all the information it needs from
the `Preview' window: the two wires and the location of the top
wedge-pair. The calculated calibration parameters are immediately
displayed in the calibration
controls window. Finally, save your results in a calibration
file.